How you access your server can undermine any security protocols you put into place. It is recommended that you use SFTP (SSH File Transfer Protocol) and SSH (Secure Shell) access to directly access your server and files. These are secure versions of the common FTP and Telnet protocols. SFTP and SSH will send passwords in an encrypted format whereas FTP and Telnet send them in plaintext.
You can find out more about these protocols at Wikipedia.com
Root or Super User accounts are a necessity if you maintain your own server but they are a security nightmare. You should never access your server directly with a Root Account unless you can absolutely guarantee a secure tunnel between your access point and the server itself. You can do this with a Virtual Private Networking protocol on both your server and the computer you access the server with. Not all servers will support this though and your datacenter might not allow the installation of the software to allow it.
If you are using Linux or Unix, you can create a usergroup called a "Wheel Group". This is a group of users that once logged in through SSH, can issue a command to switch to a superuser. This is the only way you should access your superuser accounts without a VPN connection. You can find information on creating wheel account users in your operating system's documentation.